[Paraview] segmentation fault with netCDF when loading state file

[Ryan Abernathey]

Does anyone have any feedback on this issue?

I have no idea how to debug or continue. I will have to abandon paraview
for my project unless I can get some help somehow.

Thanks,

Ryan Abernathey
Assistant Professor
Columbia University, Department of Earth & Environmental Sciences
Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
205 C Oceanography
61 Route 9W - PO Box 1000
Palisades, NY 10964-8000
http://rabernat.github.io
rpa at ldeo.columbia.edu


On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <ryan.abernathey at gmail.com>
wrote:

> Hello,
>
> I am extremely frustrated and stuck on this problem. Any advice would be
> appreciated.
>
> I am working with a dataset of 2400 sequentially numbered netCDF files
> (generic & CF conventions).
>
> In a fresh pipeline, Paraview is able to recognizes these files as a
> single source and load them correctly. I then create a standard pipeline
> involving various filters (contour, etc., nothing funny) and save a state
> file.
>
> When I attempt to load the state file, I get the following segmentation
> fault. Further down you can see a ncdump of the offending file.
>
> Would appreciate any advice on how to debug / overcome this issue. Is it a
> bug? It sure feels like one...
>
> Best,
> Ryan Abernathey
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
> line 822
> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
> dimension bound
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
> (0x8141700)
>   Debug: Off
>   Modified Time: 999905
>   Reference Count: 1
>   Registered Events: (none)
>   Request: REQUEST_DATA
>   FORWARD_DIRECTION: 0
>   FROM_OUTPUT_PORT: 0
>   ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkCompositeDataPipeline (0x744fde0): Algorithm
> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
> (0x5737250)
>   Debug: Off
>   Modified Time: 999943
>   Reference Count: 1
>   Registered Events: (none)
>   Request: REQUEST_DATA_OBJECT
>   FORWARD_DIRECTION: 0
>   FROM_OUTPUT_PORT: 0
>   ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> Segmentation fault (core dumped)
>
>
>
>
>
> ------------------------
> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_0000000300.nc
> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_0000000300 {
> dimensions:
>     x = 512 ;
>     y = 512 ;
>     z = 64 ;
>     time = UNLIMITED ; // (1 currently)
> variables:
>     float x(x) ;
>         x:units = "m" ;
>     float y(y) ;
>         y:units = "m" ;
>     float z(z) ;
>         z:units = "m" ;
>         z:long_name = "height" ;
>     float time(time) ;
>         time:units = "d" ;
>         time:long_name = "time" ;
>     float p(z) ;
>         p:units = "mb" ;
>         p:long_name = "pressure" ;
>     float zi(z) ;
>         zi:units = "m" ;
>         zi:long_name = "intfc_ht" ;
>     float U(time, z, y, x) ;
>         U:long_name = "X Wind
> Component                                                                " ;
>         U:units = "m/s       " ;
>     float V(time, z, y, x) ;
>         V:long_name = "Y Wind
> Component                                                                " ;
>         V:units = "m/s       " ;
>     float W(time, z, y, x) ;
>         W:long_name = "Z Wind
> Component                                                                " ;
>         W:units = "m/s       " ;
>     float PP(time, z, y, x) ;
>         PP:long_name = "Pressure
> Perturbation                                                           " ;
>         PP:units = "Pa        " ;
>     float QRAD(time, z, y, x) ;
>         QRAD:long_name = "Radiative heating
> rate                                                          " ;
>         QRAD:units = "K/day     " ;
>     float TABS(time, z, y, x) ;
>         TABS:long_name = "Absolute
> Temperature                                                            " ;
>         TABS:units = "K         " ;
>     float QV(time, z, y, x) ;
>         QV:long_name = "Water
> Vapor                                                                     "
> ;
>         QV:units = "g/kg      " ;
>     float QN(time, z, y, x) ;
>         QN:long_name = "Non-precipitating Condensate
> (Water+Ice)                                        " ;
>         QN:units = "g/kg      " ;
>     float QP(time, z, y, x) ;
>         QP:long_name = "Precipitating Water
> (Rain+Snow)                                                 " ;
>         QP:units = "g/kg      " ;
>     float LQRAD(time, z, y, x) ;
>         LQRAD:long_name = "LW Radiative heating
> rate                                                       " ;
>         LQRAD:units = "K/day     " ;
>     float SQRAD(time, z, y, x) ;
>         SQRAD:long_name = "SW Radiative heating
> rate                                                       " ;
>         SQRAD:units = "K/day     " ;
> }
>
>
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